Identification of Mammalian microRNA Host Genes and Transcription Units
Abstract
To derive a global perspective on the transcription of microRNAs (miRNAs) in mammals, we annotated the genomic position and context of this class of noncoding RNAs (ncRNAs) in the human and mouse genomes. Of the 232 known mammalian miRNAs, we found that 161 overlap with 123 defined transcription units (TUs). We identified miRNAs within introns of 90 protein-coding genes with a broad spectrum of molecular functions, and in both introns and exons of 66 mRNA-like noncoding RNAs (mlncRNAs). In addition, novel families of miRNAs based on host gene identity were identified. The transcription patterns of all miRNA host genes were curated from a variety of sources illustrating spatial, temporal, and physiological regulation of miRNA expression. These findings strongly suggest that miRNAs are transcribed in parallel with their host transcripts, and that the two different transcription classes of miRNAs (`exonic' and `intronic') identified here may require slightly different mechanisms of biogenesis.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Many miRNAs located within protein-coding and nonprotein-coding genes are transcriptionally linked to the expression of their host genes.
“Many miRNAs located within protein-coding and nonprotein-coding genes are transcriptionally linked to the expression of their host genes (Rodriguez et al. 2004).”
From MicroRNA expression in the adult mouse central nervous system (2008) · cites this paper as Rodriguez et al. 2004
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Sempere, L. F., Freemantle, S., Pitha-Rowe, I., Moss, E., Dmitrovsky, E., & Ambros, V. (2004) · Genome Biology · doi:10.1186/gb-2004-5-3-r13 · Cited by 1,578 · see citing works
Complete sequencing and characterization of 21,243 full-length human cDNAs
Ota, T., Suzuki, Y., Nishikawa, T., Otsuki, T., Sugiyama, T., Irie, R., Wakamatsu, A., Hayashi, K., Sato, H., Nagai, K., et al. (2004) · Nature Genetics · doi:10.1038/ng1285 · Cited by 925 · see citing works
Flagged first, then by citations
Research works printed but not linked: 4
- Hong, Y.K., Ontiveros, S.D., Chen, C., and Strauss, W.M. 1999. A new structure for the murine Xist gene and its relationship to chromosome choice/counting during X-chromosome inactivation. Proc. Natl. Acad. Sci. 96: 6829-6834.
- Kim, J., Krichevsky, A., Grad, Y., Hayes, G.D., Kosik, K.S., Church, G.M., and Ruvkun, G. 2004. Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc. Natl. Acad. Sci. 101: 360-365.
- Su, A.I., Cooke, M.P., Ching, K.A., Hakak, Y., Walker, J.R., Wiltshire, T., Orth, A.P., Vega, R.G., Sapinoso, L.M., Moqrich, A., et al. 2002. Large-scale analysis of the human and mouse transcriptomes. Proc. Natl. Acad. Sci. 99: 4465-4470.
- Yamamoto, K., Cox, J.P., Friedrich, T., Christie, P.T., Bald, M., Houtman, P.N., Lapsley, M.J., Patzer, L., Tsimaratos, M., Van, T.H.W.G., et al. 2000. Characterization of renal chloride channel (CLCN5) mutations in Dent's disease. J. Am. Soc. Nephrol. 11: 1460-1468. WEB SITE REFERENCES http://biobases.ibch.poznan.pl/ncRNA/; Noncoding RNAs database. http://www.bioinfo.rpi.edu/applications/mfold/; mfold RNA program. http://www.ensembl.org; ENSEMBL genome viewer. http://expression.gnf.org/cgi-bin/index.cgi; Gene expression atlas database. http://fantom2.gsc.riken.go.jp/; FANTOM functional annotation database. http://fatigo.bioinfo.cnio.es/; FatiGO Data Mining with Gene Ontology Terms. http://www.ncbi.nlm.nih.gov/mapview/; NCBI genome viewer. http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/; NCBI Acembly AceView gene collection. http://www.nedo.go.jp/bio-e/; Full-Length Japan database. http://read.gsc.riken.go.jp/; RIKEN expression array database. http://www.sanger.ac.uk/Software/Rfam/mirna/; miRNA Registry. http://us.expasy.org/sprot/; SWISS-PROT. http://vega.sanger.ac.uk/Homo_sapiens/; Vega human annotation browser. http://www.geneontology.org/; Gene Ontology.
Cited by
Sorted by citations
Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis
Chang, T.-C., Wentzel, E. A., Kent, O. A., Ramachandran, K., Mullendore, M., Lee, K. H., Feldmann, G., Yamakuchi, M., Ferlito, M., Lowenstein, C. J., et al. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.05.010 · Cited by 2,010 · see citing works
MicroRNA-33 and the SREBP Host Genes Cooperate to Control Cholesterol Homeostasis
Najafi-Shoushtari, S. H., Kristo, F., Li, Y., Shioda, T., Cohen, D. E., Gerszten, R. E., & Näär, A. M. (2010) · Science · doi:10.1126/science.1189123 · Cited by 957 · see citing works
The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a
Guil, S., & Cáceres, J. F. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1250 · Cited by 567 · see citing works
Circulating microRNAs as novel biomarkers for diabetes mellitus
Guay, C., & Regazzi, R. (2013) · Nature Reviews Endocrinology · doi:10.1038/nrendo.2013.86 · Cited by 563 · see citing works
Lu, Y., Zhao, X., Liu, Q., Li, C., Graves-Deal, R., Cao, Z., Singh, B., Franklin, J. L., Wang, J., Hu, H., et al. (2017) · Nature Medicine · doi:10.1038/nm.4424 · Cited by 425 · see citing works
MicroRNA expression in the adult mouse central nervous system
Bak, M., Silahtaroglu, A., Møller, M., Christensen, M., Rath, M. F., Skryabin, B., Tommerup, N., & Kauppinen, S. (2008) · RNA · doi:10.1261/rna.783108 · Cited by 463 · see citing works
MicroRNA-1 and microRNA-133a expression are decreased during skeletal muscle hypertrophy
McCarthy, J. J., & Esser, K. A. (2007) · Journal of Applied Physiology · doi:10.1152/japplphysiol.00932.2006 · Cited by 423 · see citing works
Trials and Tribulations of MicroRNA Therapeutics
Seyhan, A. A. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25031469 · Cited by 381 · see citing works
MicroRNA-regulated pathways associated with endometriosis
Ohlsson Teague, E. M. C., Van der Hoek, K. H., Van der Hoek, M. B., Perry, N., Wagaarachchi, P., Robertson, S. A., Print, C. G., & Hull, L. M. (2009) · Molecular Endocrinology · doi:10.1210/me.2008-0387 · Cited by 357 · see citing works
Guo, S.-W. (2009) · Molecular Human Reproduction · doi:10.1093/molehr/gap064 · Cited by 328 · see citing works
The role of microRNAs in endometriosis and associated reproductive conditions
Ohlsson Teague, E. M. C., Print, C. G., & Hull, M. L. (2010) · Human Reproduction Update · doi:10.1093/humupd/dmp034 · Cited by 309 · see citing works
Heme is involved in microRNA processing
Faller, M., Matsunaga, M., Yin, S., Loo, J. A., & Guo, F. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1182 · Cited by 295 · see citing works
Noncoding <scp>RNA</scp>s in disease
Lekka, E., & Hall, J. (2018) · FEBS Letters · doi:10.1002/1873-3468.13182 · Cited by 251 · see citing works
miR‐155 as a multiple sclerosis–relevant regulator of myeloid cell polarization
Moore, C. S., Rao, V. T. S., Durafourt, B. A., Bedell, B. J., Ludwin, S. K., Bar‐Or, A., & Antel, J. P. (2013) · Annals of Neurology · doi:10.1002/ana.23967 · Cited by 219 · see citing works
Adlakha, Y. K., & Saini, N. (2014) · Molecular Cancer · doi:10.1186/1476-4598-13-33 · Cited by 213 · see citing works
General Principals of miRNA Biogenesis and Regulation in the Brain
O'Carroll, D., & Schaefer, A. (2013) · Neuropsychopharmacology · doi:10.1038/npp.2012.87 · Cited by 205 · see citing works
MiR-137: an important player in neural development and neoplastic transformation
Mahmoudi, E., & Cairns, M. J. (2017) · Molecular Psychiatry · doi:10.1038/mp.2016.150 · Cited by 198 · see citing works
The roles of microRNAs in mouse development
DeVeale, B., Swindlehurst-Chan, J., & Blelloch, R. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-020-00309-5 · Cited by 121 · see citing works
Everything you wanted to know about small RNA but were afraid to ask
Boyd, S. D. (2008) · Laboratory Investigation · doi:10.1038/labinvest.2008.32 · Cited by 108 · see citing works
A Comparative Review of microRNA Expression Patterns in Autism Spectrum Disorder
Hicks, S. D., & Middleton, F. A. (2016) · Frontiers in Psychiatry · doi:10.3389/fpsyt.2016.00176 · Cited by 103 · see citing works
Evolution of small nucleolar RNAs in nematodes
Zemann, A., op de Bekke, A., Kiefmann, M., Brosius, J., & Schmitz, J. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl359 · Cited by 95 · see citing works
Plomin, R., & Davis, O. S. P. (2009) · Journal of Child Psychology and Psychiatry · doi:10.1111/j.1469-7610.2008.01978.x · Cited by 59 · see citing works
miR-124: A Promising Therapeutic Target for Central Nervous System Injuries and Diseases
Xu, J., Zheng, Y., Wang, L., Liu, Y., Wang, X., Li, Y., & Chi, G. (2022) · Cellular and Molecular Neurobiology · doi:10.1007/s10571-021-01091-6 · Cited by 55 · see citing works
Tang, W., Tang, J., He, J., Zhou, Z., Qin, Y., Qin, J., Li, B., Xu, X., Geng, Q., Jiang, W., et al. (2015) · Journal of Cellular and Molecular Medicine · doi:10.1111/jcmm.12454 · Cited by 43 · see citing works
Ciuculete, D. M., Voisin, S., Kular, L., Jonsson, J., Rask-Andersen, M., Mwinyi, J., & Schiöth, H. B. (2020) · Clinical Epigenetics · doi:10.1186/s13148-020-00884-8 · Cited by 35 · see citing works
MicroRNAs as Regulators of Phagocytosis
Gierlikowski, W., & Gierlikowska, B. (2022) · Cells · doi:10.3390/cells11091380 · Cited by 25 · see citing works
MicroRNAs in brain cholesterol metabolism and their implications for Alzheimer's disease
Yoon, H., Flores, L. F., & Kim, J. (2016) · Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids · doi:10.1016/j.bbalip.2016.04.020 · Cited by 23 · see citing works
“miRNA genes are located within various regions of the genome, including introns of protein-coding genes [86].”
Background
- Authors
- Rodriguez, A., Griffiths-Jones, S., Ashurst, J. L., & Bradley, A.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2004-09-13
- Volume
- 14
- Issue
- 10a
- Pages
- 1902-1910
- ISSN
- 1088-9051
- Cited by
- 1,732
- References
- 2
- Language
- en
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
